Proteins are dynamic and flexible biological macromolecules showing a high potential to influence the performance within both biological and industrial applications. In our research project, we are exploring the potentials of wheat gluten proteins to form secondary structures, aggregate and polymerize and we are focusing specifically on the protein α-gliadin. Gliadin proteins possess unique viscoelastic and film forming properties similar to those of petroleum based low density polypropylene materials. The α-gliadin protein is an intrinsically disordered protein, meaning that it has no distinct structure. However we know that when gliadin proteins are modified with additives like glycerol, urea and NH4OH and molded at a high temperature, they show hierarchical arrangements in the form of hexagonal nano-structures. To validate our results we will use data from recent measurements of pure samples of the protein. In order to study the α-gliadin protein we use Monte Carlo derived models and simulate its behavior when exposed to several different experimental treatments. These treatments include addition of chemical additives, modified temperature and pressure regimes, altered pH and introduction of disulphide bonds. Recently we have obtained results from Light scattering, Circular dichroism and Infra-red scattering with pure samples of the protein, showing information related to the proteins size and secondary structure. With the hereby applied computer time, we plan to use Molecular Dynamics, Monte Carlo and Quantum Mechanics methods to simulate structures, shapes and properties of the protein.
The diverse structure of the protein is the main interest of our research, in order to understand connections between structure and functionality of the protein. We aim to evaluate alterations of the protein structure at different treatments as well as options to activate specific amino acids, like cysteines, making them accessible for chemical reactions. It is known that the protein can polymerize, somehow, by forming disulphide bonds, and it is also known that disulphide bonds in proteins in general can have stabilizing effects.
Due to the disordered properties of the protein, a range of Monte Carlo derived models was used as a starting material in our studies, to secure statistically significant variations in our modelled proteins. The effect of modelling an introduction of disulphide bonds for the disordered properties of the protein is still not understood, thus we will focus on these characters when running molecular dynamics experiments.
Some part of the allocated time might also be consumed for calibration and sensitivity analyses of the models. These simulations are aimed to test the effect of force fields.
We hope that you find our application for using the HPC2N Kebnekaise resource including the GPU nodes in order to investigate the α-gliadin protein, of relevance